I think it's the same case as sebbio, but more global.
When the notification manager element size change (floating window resize/move, browser resize...), linked notifications are not moved to match the new element position/size.
In case of browser resize, notifications can be out of screen. If there is a notification with "autoDestroy: false" out of screen, newer positions based on sibling position are all out of screen.

I think replacing all instances of me.hide() with me.close() in the code is the way to improve it (I haven't tried it). The default closeAction of a window is destroy. So, when you close() a window, the instance is destroyed.